From owner-chemistry@ccl.net Wed May 28 03:40:00 2008 From: "Ulrich Scharfenort scharfenort(a)ltt.rwth-aachen.de" To: CCL Subject: CCL:G: G Polarizibiliy at imaginary Frequencies Message-Id: <-37049-080527024213-23664-xr8BkJQfHNXh0DJBtskzIA\a/server.ccl.net> X-Original-From: Ulrich Scharfenort Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 27 May 2008 08:41:50 +0200 MIME-version: 1.0 Sent to CCL by: Ulrich Scharfenort [scharfenort|*|ltt.rwth-aachen.de] Hello, is it possible to calculate polarizibilities with Gaussian03 at imaginary frequencies? If possible: How does an input file for this task looking? Thanks Ulrich Scharfenort From owner-chemistry@ccl.net Wed May 28 04:39:01 2008 From: "Sina T reli sinatureli{}gmail.com" To: CCL Subject: CCL: Floating Point Math Errors Message-Id: <-37050-080528043432-11790-/kQqxWRPtXBwAsOfnTCXPg.:.server.ccl.net> X-Original-From: "Sina T reli" Date: Wed, 28 May 2008 04:34:27 -0400 Sent to CCL by: "Sina T reli" [sinatureli%a%gmail.com] Hello, I am working on a project related to proteins and my precision for coordinates is there digits after the dot. When I do operations like rotation around a dihedral, the dihedrals which shouldn't change change at about 0.01 angles and so. I am afraid though that is not much it might accumulate over time. So do you have any suggestions for reducing floating integer errors? Would't be feasible if I turned lets say the coordinate 21.567 to 21567 and do my operations? Or maybe even 215670? Thanks From owner-chemistry@ccl.net Wed May 28 09:16:01 2008 From: "gajuguard-ccl{:}yahoo.co.in" To: CCL Subject: CCL: Which Drug Design s/w to be Bought for Academic Research Message-Id: <-37051-080527095202-5690-bP80qyjeyaNQQXdqqsnzsg.@.server.ccl.net> X-Original-From: gajuguard-ccl::yahoo.co.in Content-Type: multipart/alternative; boundary="0-901870661-1211892705=:80958" Date: Tue, 27 May 2008 18:21:45 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: gajuguard-ccl^^^yahoo.co.in --0-901870661-1211892705=:80958 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Respected Sir / Madam,   Our's is the Pharmacy Dept in the SGSITS, an Autonomous Institute in MP, IN= DIA. We are in process to buy a drug design software for the purpose of doing ba= sic research in drug design (non-profit purpose) for - QSAR - Docking=20 - Pharmacophore modeling - prediction of ADME parameters=20 - & other accessories   So, we are in search of a drug design software to be bought in thedept't&nb= sp;which is economic, with out time limitation, with neccessary accura= ry & predictability in results for academic research.   Kindly have some suggestions.   Thanking you.   Sincerely, Gajanan Wanare, Dept't of Pharmacy, Shri G S Institute of Technology & Science (SGSITS), Indore- (MP) INDIA. www.sgsits.ac.in gajuguard-ccl---yahoo.co.in=0A=0A=0A Best Jokes, Best Friends, Best Food= and more. Go to http://in.promos.yahoo.com/groups/bestofyahoo/ --0-901870661-1211892705=:80958 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Re= spected Sir / Madam,
 
Our's is the Pharmacy Dept in the SGSITS, an Autonomous Institute in M= P, INDIA.
We are in process to buy a drug design software for the purpose of doi= ng basic research in drug design (non-profit purpose) for
- QSAR
- Docking
- Pharmacophore modeling
- prediction of ADME parameters
- & other accessories
 
So, we are in search of a drug design software to be bought in thedept= 't which is economic, with out time limitation, with neccessary a= ccurary & predictability in results for academic research.
 
Kindly have some suggestions.
 
Thanking you.
 
Sincerely,
Gajanan Wanare,
Dept't of Pharmacy,
Shri G S Institute of Technology & Science (SGSITS),
Indore- (MP) INDIA.

=0A=0A=0A
= Best Jokes, Best Friends, Best Food. Get all this and more on Best of Yahoo! Groups. --0-901870661-1211892705=:80958-- From owner-chemistry@ccl.net Wed May 28 09:51:01 2008 From: "Peter Bladon p.bladon~~strath.ac.uk" To: CCL Subject: CCL: Unambigous comparison of 3D structures Message-Id: <-37052-080527181926-10041-FWMCCfQjw99NiXxqmOuQ6g|a|server.ccl.net> X-Original-From: "Peter Bladon" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 27 May 2008 22:39:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Peter Bladon" [p.bladon]^[strath.ac.uk] Dear David =20 There are facilities in the Interprobe software for doing some of the = tasks;=20 they might need to be adapted if your aim is to do large numbers of = comparisons. The program called PROTEINS will abstract individual structures = (including the ligands) from the PDB, in a form that will allow you to separate the = ligand from the protein using the program INTERCHEM. The programs THREEDOM allows different poses of a single ligand (or = different ligands) to be superimposed. The superimposition does not require any atom to = atom correlations,=20 nor on the corresponding atoms in different poses being ordered in the = same way. It relies entirely on the overall shapes of the poses. It will fail in = extreme cases where the poses are very different, or where the shape of the ligand has some = apparent symmetry.=20 In general the superimposition will give you a measure of the = similarity of the poses.=20 =20 Because the PDB structures do not usually have hydrogens, you will need = a method of=20 adding hydrogens. The program INTERCHEM will allow you to remove = hydrogens (this would suffice in preliminary trials). =20 If you need help or further explananations please contact me. =20 Dr. Peter Bladon Interprobe Chemical Services Telephone: +44-(0)141-578-1109 Facsimile: +44-(0)141-776-7712 e-mail: cbas25*o*strath.ac.uk URL: http://www.interprobe.co.uk/interprobe.html =20 =20 ________________________________ > From: David D phrm75{:}yahoo.com [mailto:owner-chemistry*o*ccl.net] Sent: Thu 22-May-08 21:34 To: Bladon, Peter Subject: CCL: Unambigous comparison of 3D structures Hello, I need to perform analysis changes in 3D structures of small molecules = in different PDB files. One way of doing this is to superimpose the = molecules. The problem is that superposition algorithms need user input = of paired atoms. Otherwise, unattended superposition results may depend = on the initial orientation of the two molecules. Superposition is = especially problematic in the case of molecules with multiple symmetry = axes. Another possibility is to create connectivity matrix file = (Z-matrix) that will contain molecules internal coordinates. Here, = unattended processes rely heavily on the order of the atoms in the = original PDB file. Thus, my questions are: - am I wrong in any of the above statements? - is there any way to bring to structures of small molecules to a = "common denominator" that will enable reliable analysis of the 3D = structure changes? - all the files originate from the PDB. Are there internal standards = that enable unattended creation of Z-matrices? Assumptions: - only chemically identical structures are compared. - all the structures will be downloaded from the PDB Thank you From owner-chemistry@ccl.net Wed May 28 10:34:00 2008 From: "andras.borosy#%#givaudan.com" To: CCL Subject: CCL: activation energy barriers of DA cycloadditons in organic solvents catalysed by Lewis acids? Message-Id: <-37053-080528092546-15700-9blRTthdKrhL5CmIgEtDLQ{=}server.ccl.net> X-Original-From: andras.borosy*givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 00436AD4C1257457_=" Date: Wed, 28 May 2008 14:16:22 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy-.-givaudan.com This is a multipart message in MIME format. --=_alternative 00436AD4C1257457_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, Where can I find reliable experimental (or calculated) activation energy=20 barriers of DA cycloadditons in organic solvents catalysed by Lewis=20 acids? Many thank, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com --=_alternative 00436AD4C1257457_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

Where can I find reliable experiment= al (or calculated)  activation energy barriers of DA cycloadditons  = in organic solvents catalysed by Lewis acids?

Many thank,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com
--=_alternative 00436AD4C1257457_=-- From owner-chemistry@ccl.net Wed May 28 11:30:01 2008 From: "Maxim Kholin maxim.kholin[-]q-pharm.com" To: CCL Subject: CCL: Which Drug Design s/w to be Bought for Academic Research Message-Id: <-37054-080528112101-25627-yiqhJmvx8LTZodidpisMeg[-]server.ccl.net> X-Original-From: "Maxim Kholin" Content-Type: multipart/alternative; boundary="----=_NextPart_000_04D9_01C8C0EF.B1163B00" Date: Wed, 28 May 2008 18:21:48 +0400 MIME-Version: 1.0 Sent to CCL by: "Maxim Kholin" [maxim.kholin/./q-pharm.com] This is a multi-part message in MIME format. ------=_NextPart_000_04D9_01C8C0EF.B1163B00 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Dr. Wanare, Let me suggest you looking at www.q-lead.com where Quantum software = modules are described. The most of the areas of your interest is covered. Speical Academia = terms are available. In many terms the Quantum software is unique using new generation = approaches. Maxim Kholin ----- Original Message -----=20 From: gajuguard-ccl{:}yahoo.co.in=20 To: Kholin, Maxim N =20 Sent: Tuesday, May 27, 2008 4:51 PM Subject: CCL: Which Drug Design s/w to be Bought for Academic Research Respected Sir / Madam, Our's is the Pharmacy Dept in the SGSITS, an Autonomous = Institute in MP, INDIA. We are in process to buy a drug design software for the purpose = of doing basic research in drug design (non-profit purpose) for - QSAR - Docking=20 - Pharmacophore modeling - prediction of ADME parameters=20 - & other accessories So, we are in search of a drug design software to be bought in = thedept't which is economic, with out time limitation, with neccessary = accurary & predictability in results for academic research. Kindly have some suggestions. Thanking you. Sincerely, Gajanan Wanare, Dept't of Pharmacy, Shri G S Institute of Technology & Science (SGSITS), Indore- (MP) INDIA. www.sgsits.ac.in gajuguard-ccl(_)yahoo.co.in=20 -------------------------------------------------------------------------= ----- Best Jokes, Best Friends, Best Food. Get all this and more on Best of = Yahoo! Groups. ------=_NextPart_000_04D9_01C8C0EF.B1163B00 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable =EF=BB=BF
Dear Dr. Wanare,
Let me suggest you looking at www.q-lead.com where Quantum = software=20 modules are described.
The most of the areas of your interest = is covered.=20 Speical Academia terms are available.
In many terms the Quantum software is = unique using=20 new generation approaches.
 
Maxim Kholin
 
 
----- Original Message -----
From:=20 gajuguard-ccl{:}yahoo.co.in =
Sent: Tuesday, May 27, 2008 = 4:51 PM
Subject: CCL: Which Drug Design = s/w to be=20 Bought for Academic Research

Respected Sir / Madam,
 
Our's is the Pharmacy Dept in the SGSITS, an Autonomous = Institute=20 in MP, INDIA.
We are in process to buy a drug design software for the = purpose of=20 doing basic research in drug design (non-profit purpose) = for
- QSAR
- Docking
- Pharmacophore modeling
- prediction of ADME parameters
- & other accessories
 
So, we are in search of a drug design software to be bought = in=20 thedept't which is economic, with out time limitation, = with=20 neccessary accurary & predictability in results for academic = research.
 
Kindly have some suggestions.
 
Thanking you.
 
Sincerely,
Gajanan Wanare,
Dept't of Pharmacy,
Shri G S Institute of Technology & Science = (SGSITS),
Indore- (MP) INDIA.
gajuguard-ccl(_)yahoo.co.in


Best Jokes, Best Friends, Best Food. Get all this and more on Best=20 of Yahoo! Groups. ------=_NextPart_000_04D9_01C8C0EF.B1163B00-- From owner-chemistry@ccl.net Wed May 28 12:04:00 2008 From: "Zsolt Zsoldos zsolt _ simbiosys.ca" To: CCL Subject: CCL: Floating Point Math Errors Message-Id: <-37055-080528113800-2596-BCOM5bCjPFQzp5iPbhqvmQ~!~server.ccl.net> X-Original-From: "Zsolt Zsoldos" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 28 May 2008 10:40:23 -0400 MIME-Version: 1.0 Sent to CCL by: "Zsolt Zsoldos" [zsolt{=}simbiosys.ca] Hello, The short answer is: fixed point representation can help to eliminate floating point errors in some cases, but not for the case of rotation. I have put a detailed explanation to answer this question on my blog with some example code as well. It is too long to post here, so I only include the URL: http://www.simbiosys.ca/blog/ Zsolt > Sent to CCL by: "Sina T reli" [sinatureli%a%gmail.com] > Hello, > > I am working on a project related to proteins and my precision for coordinates > is there digits after the dot. When I do operations like rotation around a > dihedral, the dihedrals which shouldn't change change at about 0.01 angles > and so. I am afraid though that is not much it might accumulate over time. So > do you have any suggestions for reducing floating integer errors? Would't be > feasible if I turned lets say the coordinate 21.567 to 21567 and do my > operations? Or maybe even 215670? > -- Zsolt Zsoldos, PhD http://www.simbiosys.ca/ From owner-chemistry@ccl.net Wed May 28 15:15:00 2008 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli.:.gmail.com" To: CCL Subject: CCL: Floating Point Math Errors Message-Id: <-37056-080528151225-8144-6zc0y7WygBR78CT8N6bbCQ#server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_32984_20562670.1212001905355" Date: Wed, 28 May 2008 22:11:45 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli**gmail.com] ------=_Part_32984_20562670.1212001905355 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thanks for the answer On Wed, May 28, 2008 at 5:40 PM, Zsolt Zsoldos zsolt _ simbiosys.ca < owner-chemistry-.-ccl.net> wrote: > > Sent to CCL by: "Zsolt Zsoldos" [zsolt{=}simbiosys.ca] > Hello, > > The short answer is: fixed point representation can help to eliminate > floating point errors in some cases, but not for the case of rotation. > I have put a detailed explanation to answer this question on my blog > with some example code as well. It is too long to post here, so I only > include the URL: > http://www.simbiosys.ca/blog/ > > Zsolt > > > Sent to CCL by: "Sina T reli" [sinatureli%a%gmail.com] > > Hello, > > > > I am working on a project related to proteins and my precision for > coordinates > > is there digits after the dot. When I do operations like rotation around > a > > dihedral, the dihedrals which shouldn't change change at about 0.01 > angles > > and so. I am afraid though that is not much it might accumulate over > time. So > > do you have any suggestions for reducing floating integer errors? Would't > be > > feasible if I turned lets say the coordinate 21.567 to 21567 and do my > > operations? Or maybe even 215670? > > > > -- > Zsolt Zsoldos, PhD http://www.simbiosys.ca/> > > -- "Vectors have never been of the slightest use to any creature. Quaternions came from Hamilton after his really good work had been done; and though beautifully ingenious, have been an unmixed evil to those who have touched them in any way, including Maxwell." - Lord Kelvin ------=_Part_32984_20562670.1212001905355 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thanks for the answer

On Wed, May 28, 2008 at 5:40 PM, Zsolt Zsoldos zsolt _ simbiosys.ca <owner-chemistry-.-ccl.net> wrote:

Sent to CCL by: "Zsolt Zsoldos" [zsolt{=}simbiosys.ca]
Hello,

The short answer is: fixed point representation can help to eliminate
floating point errors in some cases, but not for the case of rotation.
I have put a detailed explanation to answer this question on my blog
with some example code as well. It is too long to post here, so I only
include the URL:
http://www.simbiosys.ca/blog/

Zsolt

> Sent to CCL by: "Sina  T  reli" [sinatureli%a%gmail.com]
> Hello,
>
> I am working on a project related to proteins and my precision for coordinates
> is there digits after the dot. When I do operations like rotation around a
> dihedral, the dihedrals which shouldn't change change at about 0.01 angles
> and so. I am afraid though that is not much it might accumulate over time. So
> do you have any suggestions for reducing floating integer errors? Would't be
> feasible if I turned lets say the coordinate 21.567 to 21567 and do my
> operations? Or maybe even 215670?
>

--
Zsolt Zsoldos, PhD    http://www.simbiosys.ca/



--
"Vectors have never been of the slightest use to any creature. Quaternions came from Hamilton after his really good work had been done; and though beautifully ingenious, have been an unmixed evil to those who have touched them in any way, including Maxwell." - Lord Kelvin ------=_Part_32984_20562670.1212001905355--